Homeobox containing genes are a family of genes which have been shown in Drosophila to control pattern formation during development. These genes encode proteins which bind to DNA in a sequence specific manner. They contain a 180 bp conserved DNA domain called a homeobox. We have isolated several homeobox containing genes which are activated during early Xenopus development. We have determined their temporal and spatial expression pattern using Northern blot analysis and in situ hybridization. At least some of these genes are expressed during gastrulation, a critical time period of development at which mesodermal and neural induction takes place. Sequence analysis of these genes revealed that some of them are homologous to previously described genes in other species such as mouse and Drosophila, others have not yet been described. One of the new homeobox genes, the XDLL- 1, is homologous to Drosophila Distal-less gene family. It is expressed in the embryonic cement gland, neural crest derived visceral arches and forebrain. Its temporospatial expression pattern indicates that this gene is involved in forebrain and cranio-facial development. In addition to the homeobox gene family we have isolated new members of the Fork head gene family. The individual members of this family have a highly interesting expression pattern and at least some of them are oncogenes. The first Xenopus Fork head gene XFKH1 has many highly interesting features. It is activated at, or shortly after, the mid-blastula transition in the dorsal marginal bone of the embryo. In early gastrulae it is restricted to the organizer region. At later stages it is expressed in the notochord and neural organizer region. Furthermore, it is inducible by activin in isolated animal caps. Its expression pattern and inducibility by activin suggests that this gene has a critical importance for early pattern formation in Xenopus embryos. Its expression pattern and inducibility by activin suggests that this gene has a critical importance for early pattern formation in Xenopus embryos. We have shown that this gene belongs to a larger family of Fork head genes, which, like homeobox genes are involved in different aspects of pattern formation and cell differentiation. In addition, we have initiated similar research into pattern formation in Zebrafish embryos.